VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Thu Mar 23 2006 - 16:17:29 CST

FYI:

This guy provides a nice explanation of the Kabsch algorithm:
http://www.dillgroup.ucsf.edu/~bosco/rmsd.html

For John:
And he states he has written his own optimal superposition code (which
is also based on Kabsch).
If he didn't just copy-paste the code from pymol or vmd, it might be
useful for comparison:
http://www.dillgroup.ucsf.edu/~bosco/code.html#rmsd

John Stone wrote:

>Jan,
> VMD and PyMol are (or at least were) using the same exact
>RMS fit code. VMD actually has two implementations, both derived
>from Kabsch, so they fall down in about the same way, but in different
>cases. I agree it would be interesting to collect info from other
>people's experiences with other packages, but thought I'd mention
>that the PyMol / VMD RMS fit code should actually be the same.
>You can switch which code VMD uses by setting and environment variable
>that I don't recall off the top of my head BTW. It's mentioned in the
>User's Guide.
>
> John
>
>On Thu, Mar 23, 2006 at 10:30:53PM +0100, Jan Saam wrote:
>
>
>>Hi all,
>>
>>I've noticed this behaviour in several cases, too. It seems to be a
>>limitation of the algorithm due to Kabsch 1976. For small sets of atoms
>>(~<100) the rotation sometimes is just wrong.
>>
>>Does anybody know a better alignment algorithm?
>>
>>Also it would be interesting to know if the same problem also occurs in
>>Pymol or other viewers. If it works in Pymol it would be interesting to
>>see what they do better.
>>I stumbled over a reference in the internet where someone implemented
>>the Kabsch algorithm as a Pymol script. I wonder if that one aligns your
>>molecules correctly?
>>
>>IS THERE A PYMOL USER LISTENING?
>>Could you try it with Visvaldas example?
>>
>>Regards,
>>Jan
>>
>>PS.
>>That's the original paper:
>>*[Kabsch, 1976]* Kabsch, W. (1976). A solution for the best rotation to
>>relate two sets of vectors. /Acta. Crystal/, 32A:922-923.
>>
>>Did anybody read the following paper? I don't have access to it, but it
>>might contain some information about our problem:
>>*[Kabsch, 1978]* Kabsch, W. (1978). A discussion of the solution for the
>>best rotation to related two sets of vectors. /Acta. Crystal/, 34A:827-828.
>>
>>
>>
>>Visvaldas Kairys wrote:
>>
>>
>>
>>>Hi all,
>>>
>>>I am trying to use VMD to compute RMSD between selected residues, and for
>>>practical purposes I superimpose only the atoms under interest.
>>>Below is an example of molecules (in pdb format) which cause problem.
>>>
>>>molecule 1:
>>>
>>>CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>>>ATOM 1 CA GLU A 1 -29.843 154.588 35.594 0.00 0.00
>>>ATOM 2 CA GLU A 2 -27.292 160.642 36.936 0.00 0.00
>>>ATOM 3 CA GLU A 3 -32.648 156.854 50.794 0.00 0.00
>>>END
>>>
>>>molecule 2:
>>>
>>>CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>>>ATOM 1 CA GLU A 1 44.084 6.298 12.425 0.00 0.00
>>>ATOM 2 CA GLU A 2 39.046 2.420 14.373 0.00 0.00
>>>ATOM 3 CA GLU A 3 46.929 -0.875 26.932 0.00 0.00
>>>END
>>>
>>>If I open RMSD calculator extension, unselect backbone button
>>>and type "all" for atom selection, then click "Align",
>>>the molecules do not become aligned (it's pretty obvious), and "RMSD"
>>>is quite high. If I keep clicking "Align" and subsequent "RMSD",
>>>the position of atoms and RMSD keep changing.
>>>
>>>If I simply duplicate each atom in both of molecules above,
>>>yielding 6 atoms in each, the alignment and RMSD calculation proceeds
>>>correctly.
>>>
>>>I wonder if there is some formatting problem in my molecules or it is a
>>>bug.
>>>
>>>I had similar errors with two molecules consisting of 2 atoms. I didn't
>>>look
>>>carefully at other sizes of molecules, but big molecules seem to be OK.
>>>
>>>I am running VMD 1.8.4a22 on AMD64 Linux machine.
>>>
>>>Your help will be appreciated!
>>>
>>>Sincerely,
>>>
>>>Visvaldas Kairys
>>>University of Madeira
>>>Portugal
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>--
>>---------------------------
>>Jan Saam
>>Institute of Biochemistry
>>Charite Berlin
>>Monbijoustr. 2
>>10117 Berlin
>>Germany
>>
>>+49 30 450-528-446
>>saam_at_charite.de
>>
>>
>>
>
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de